Linux-cluster performance

From: Florian Barth <>
Date: Wed 15 Aug 2001 15:07:51 +0200

Dear AMBER users,

I have installed AMBER 6.0 on a Linux cluster with Mandrake 8.0
(kernel 2.4.3), mpich 1.2.1 and the latest gcc (2.96) and pgi (3.2)
compiler. The cluster consists of 4 nodes with one 1.33 GHz Athlon
CPU, 512 MB RAM and 20 GB disk space each. They are connected via
100Mbit T-baseTx switched FastEthernet.
Here are some sander benchmarks of the cluster:

prowat (11000 atoms):
nCPU time
1 86.2s
2 51.2s (x1.7)
4 36.5s (x2.4)

benchmark.6 (22000 atoms):
nCPU time
1 176.4s
2 137.6s (x1.3)
4 100.4s (x1.8)

large protein (44000 atoms):
nCPU time
1 407.3s
2 356.8s (x1.1)
4 265.9s (x1.5)

As you can notice, the scalability of the system decreases with its
size. Since I don't have any other reference system, I`m not quite
sure about the cause of this perfomance dropping. I think it might be
the slow 100Mbit connection. Maybe somebody can tell me ways (hardware
or software solutions) to enhance the scalability of large systems
with sander 6 on a cluster.

Thank you very much in advance

Florian Barth


Florian Barth
Institute of Technical Biochemistry
University of Stuttgart
Allmandring 31
70569 Stuttgart
phone: +49-711-6857481
fax: +49-711-6853196
Received on Wed Aug 15 2001 - 06:07:51 PDT
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